Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 183 of 425
Found at i:55489423 original size:79 final size:78
Alignment explanation
Indices: 55489236--55489449 Score: 225
Period size: 78 Copynumber: 2.7 Consensus size: 78
55489226 ATTGTGATAT
** *
55489236 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATGGTG
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTTGTGATATCCGGGTTAAGCCCGAAGGCAATGGTG
** *
55489301 CGAGCTATGATAT
66 CGAGCTACCATAA
** * *
55489314 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTTGTGATATCCGGGTTAAG-CCCGAAGGCAATGGT
* *
55489379 GCGGGTTACCATAA
65 GCGAGCTACCATAA
* * ** * *
55489393 CCGGGCTATGTCCGAAGGCGTTTGAACGAGTAGCT-ATATCC-GGTTAAACTCCGAAGG
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTTG-TGATATCCGGGTTAAGC-CCGAAGG
55489450 TATGTGATTT
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
77 1 0.01
78 61 0.52
79 54 0.46
80 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCAATTGAACGAGTTGTGATATCCGGGTTAAGCCCGAAGGCAATGGTG
CGAGCTACCATAA
Found at i:55491819 original size:40 final size:40
Alignment explanation
Indices: 55491734--55491884 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
55491724 AATTGAATGA
* * *
55491734 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
55491774 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
55491815 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
55491854 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
55491885 ACATGTTATA
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:55499828 original size:40 final size:40
Alignment explanation
Indices: 55499743--55499893 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
55499733 AATTGAATGA
* * *
55499743 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
55499783 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
55499824 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
55499863 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
55499894 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:55499907 original size:40 final size:40
Alignment explanation
Indices: 55499780--55499909 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
55499770 ATGCTGGAAA
* * * *
55499780 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
55499820 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
55499860 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
55499900 TTATATCCGG
1 TTATATCCGG
55499910 TTATGTTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:55503399 original size:18 final size:18
Alignment explanation
Indices: 55503357--55503391 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55503347 GTTTTACTTC
55503357 TCTATTTCTATTCCTTTT
1 TCTATTTCTATTCCTTTT
*
55503375 TCTATTTC-ATTTCTTTT
1 TCTATTTCTATTCCTTTT
55503392 ATTTATTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (18 bp):
TCTATTTCTATTCCTTTT
Found at i:55503434 original size:5 final size:5
Alignment explanation
Indices: 55503424--55503500 Score: 147
Period size: 5 Copynumber: 15.6 Consensus size: 5
55503414 AATTATTATA
55503424 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
55503474 ATAAT ATAAT ATAAT ATAAT AT-AT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
55503501 CTTAAATATT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.06
5 67 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:55503546 original size:20 final size:19
Alignment explanation
Indices: 55503521--55503568 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
55503511 AAGTATTACA
*
55503521 TATATTATTATCTACATATG
1 TATATTATT-TCTACACATG
*
55503541 TATATTATTTTTACACATG
1 TATATTATTTCTACACATG
55503560 TA-ATTATTT
1 TATATTATTT
55503569 TTACCATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATTATTTCTACACATG
Found at i:55503567 original size:18 final size:19
Alignment explanation
Indices: 55503521--55503572 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
55503511 AAGTATTACA
* *
55503521 TATATTATTATCTACATATG
1 TATATTATT-TTTACACATG
55503541 TATATTATTTTTACACATG
1 TATATTATTTTTACACATG
55503560 TA-ATTATTTTTAC
1 TATATTATTTTTAC
55503573 CATACACTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.37
19 10 0.33
20 9 0.30
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATTATTTTTACACATG
Found at i:55508058 original size:39 final size:39
Alignment explanation
Indices: 55508014--55508112 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
55508004 GAATACGAAG
* * * *
55508014 CTTGAAATTGTGTTAAACAACTTTTTCTAAGCGATTTTA
1 CTTGAAAATGAGTAAAACAACTTTTGCTAAGCGATTTTA
*
55508053 CTTGAAAATGAGTAAAACAACTTTTGCTAAGTGATTTTA
1 CTTGAAAATGAGTAAAACAACTTTTGCTAAGCGATTTTA
*
55508092 -TGTGAAAACGAGTAAAACAAC
1 CT-TGAAAATGAGTAAAACAAC
55508113 ATAATCGGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.02
39 52 0.98
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (39 bp):
CTTGAAAATGAGTAAAACAACTTTTGCTAAGCGATTTTA
Found at i:55509178 original size:18 final size:18
Alignment explanation
Indices: 55509155--55509191 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55509145 TATTTATACA
55509155 AATGATGTTTTATGTTGG
1 AATGATGTTTTATGTTGG
55509173 AATGATGTTTTATGTTGG
1 AATGATGTTTTATGTTGG
55509191 A
1 A
55509192 TTGCATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (18 bp):
AATGATGTTTTATGTTGG
Found at i:55509203 original size:18 final size:18
Alignment explanation
Indices: 55509155--55509206 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
55509145 TATTTATACA
*
55509155 AATGATGTTTTATGTTGG
1 AATGATGTATTATGTTGG
*
55509173 AATGATGTTTTATGTTGG
1 AATGATGTATTATGTTGG
*
55509191 ATTGCATG-ATTATGTT
1 AATG-ATGTATTATGTT
55509207 ACTTGCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (18 bp):
AATGATGTATTATGTTGG
Found at i:55509616 original size:27 final size:27
Alignment explanation
Indices: 55509578--55509632 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
55509568 TTATATGAGT
55509578 TTGAAAAATCATTAAAAATAGTAGAGA
1 TTGAAAAATCATTAAAAATAGTAGAGA
55509605 TTGAAAAATCATTAAAAATAGTAGAGA
1 TTGAAAAATCATTAAAAATAGTAGAGA
55509632 T
1 T
55509633 AGAATTAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.55, C:0.04, G:0.15, T:0.27
Consensus pattern (27 bp):
TTGAAAAATCATTAAAAATAGTAGAGA
Found at i:55516712 original size:18 final size:18
Alignment explanation
Indices: 55516689--55516725 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55516679 TATTTATACA
55516689 AATGATGTTTTATGTTGG
1 AATGATGTTTTATGTTGG
55516707 AATGATGTTTTATGTTGG
1 AATGATGTTTTATGTTGG
55516725 A
1 A
55516726 TTGCATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (18 bp):
AATGATGTTTTATGTTGG
Found at i:55516737 original size:18 final size:18
Alignment explanation
Indices: 55516689--55516740 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
55516679 TATTTATACA
*
55516689 AATGATGTTTTATGTTGG
1 AATGATGTATTATGTTGG
*
55516707 AATGATGTTTTATGTTGG
1 AATGATGTATTATGTTGG
*
55516725 ATTGCATG-ATTATGTT
1 AATG-ATGTATTATGTT
55516741 ACTTGCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (18 bp):
AATGATGTATTATGTTGG
Found at i:55520518 original size:47 final size:47
Alignment explanation
Indices: 55520449--55520838 Score: 586
Period size: 47 Copynumber: 8.3 Consensus size: 47
55520439 CCCTTCGGGA
* *
55520449 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
55520496 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
55520543 CTTATTACACGTATGCACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
55520590 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
55520637 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
55520683 CTTATCACATATATACACTTTCACATCCATCACATTTGCCATTCGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
55520730 CTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
55520777 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCA-GC
1 CTTATCACACATATACACTTTCACATTCATCACATTGGCCATT-AGGC
55520824 CTTATCACACATATA
1 CTTATCACACATATA
55520839 TGTATATCAT
Statistics
Matches: 305, Mismatches: 36, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
46 40 0.13
47 264 0.87
48 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACACATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:55520765 original size:187 final size:188
Alignment explanation
Indices: 55520449--55520837 Score: 726
Period size: 187 Copynumber: 2.1 Consensus size: 188
55520439 CCCTTCGGGA
55520449 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * *
55520514 TTTCACATCCATCACATTGGCCATTCGGCCTTATTACACGTATGCACTTTCACATTCATCACATG
66 TTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATG
*
55520579 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCAGC
55520637 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGG-CTTATCACATATATACAC
1 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
55520701 TTTCACATCCATCACATTTGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATG
66 TTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATG
55520766 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCAGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCAGC
55520824 CTTATCACACATAT
1 CTTATCACACATAT
55520838 ATGTATATCA
Statistics
Matches: 196, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
187 150 0.77
188 46 0.23
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATATACACTTTCACATTCATCACATG
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCAGC
Found at i:55520838 original size:94 final size:94
Alignment explanation
Indices: 55520449--55520837 Score: 690
Period size: 94 Copynumber: 4.1 Consensus size: 94
55520439 CCCTTCGGGA
55520449 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
55520514 TTTCACATCCATCACATTGGCCATTCGGC
66 TTTCACATCCATCACATTGGCCATTCGGC
* * *
55520543 CTTATTACACGTATGCACTTTCACATTCATCACATGGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
55520608 TTTCACATTCATCACATTGGCCATTCGGC
66 TTTCACATCCATCACATTGGCCATTCGGC
55520637 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGG-CTTATCACATATATACAC
1 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
55520701 TTTCACATCCATCACATTTGCCATTCGGC
66 TTTCACATCCATCACATTGGCCATTCGGC
* *
55520730 CTTATCACACATATACACTTTCACATTCATCACATGGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
55520795 TTTCACATTCATCACATTGGCCATTCAGC
66 TTTCACATCCATCACATTGGCCATTCGGC
55520824 CTTATCACACATAT
1 CTTATCACACATAT
55520838 ATGTATATCA
Statistics
Matches: 280, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
93 89 0.32
94 191 0.68
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACACATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATCCATCACATTGGCCATTCGGC
Found at i:55523868 original size:13 final size:13
Alignment explanation
Indices: 55523843--55523875 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
55523833 CTTGTCTATT
*
55523843 TTTC-TTTCTTTA
1 TTTCTTTTCATTA
55523855 TTTCTTTTCATTA
1 TTTCTTTTCATTA
55523868 TTTCTTTT
1 TTTCTTTT
55523876 TATTCCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTTCATTA
Found at i:55528551 original size:13 final size:13
Alignment explanation
Indices: 55528533--55528560 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55528523 AGATTGGAAG
55528533 TTGGTAGAATCAT
1 TTGGTAGAATCAT
55528546 TTGGTAGAATCAT
1 TTGGTAGAATCAT
55528559 TT
1 TT
55528561 CAGTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (13 bp):
TTGGTAGAATCAT
Found at i:55529063 original size:18 final size:17
Alignment explanation
Indices: 55529036--55529074 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
55529026 GTGCAAGATC
55529036 GAAAACAATTAAATTGAT
1 GAAAACAATT-AATTGAT
* *
55529054 GAAAATAATTATTTGAT
1 GAAAACAATTAATTGAT
55529071 GAAA
1 GAAA
55529075 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (17 bp):
GAAAACAATTAATTGAT
Found at i:55534092 original size:19 final size:19
Alignment explanation
Indices: 55534068--55534115 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
55534058 CTCTTATCAT
*
55534068 GTTATGGTATTGTGAACTA
1 GTTATGGCATTGTGAACTA
*
55534087 GTTATGGCCTTGTGAACTA
1 GTTATGGCATTGTGAACTA
*
55534106 ATTATGGCAT
1 GTTATGGCAT
55534116 GTAATGAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (19 bp):
GTTATGGCATTGTGAACTA
Found at i:55541452 original size:20 final size:20
Alignment explanation
Indices: 55541427--55541464 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55541417 TATGACTGTA
*
55541427 AAATTTTTCTAAGTGTTCAG
1 AAATTTTTATAAGTGTTCAG
*
55541447 AAATTTTTATATGTGTTC
1 AAATTTTTATAAGTGTTC
55541465 GGTATAGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
AAATTTTTATAAGTGTTCAG
Found at i:55548762 original size:34 final size:34
Alignment explanation
Indices: 55548707--55548815 Score: 184
Period size: 34 Copynumber: 3.2 Consensus size: 34
55548697 AGTGATAGTC
*
55548707 TAGTATCAGTGT-GGCCTTAGCCGATTACAGTAA
1 TAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
55548740 TAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
1 TAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
*
55548774 CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
1 TAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
*
55548808 AAGTATCA
1 TAGTATCA
55548816 TAAATGCAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 12 0.17
34 60 0.83
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (34 bp):
TAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
Found at i:55557783 original size:20 final size:20
Alignment explanation
Indices: 55557758--55557807 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
55557748 AAGTTTATGC
55557758 TAAGTAAATGAAATGAAAAG
1 TAAGTAAATGAAATGAAAAG
* **
55557778 TAAGTAATTGAAATGGTAAG
1 TAAGTAAATGAAATGAAAAG
*
55557798 AAAGTAAATG
1 TAAGTAAATG
55557808 GAGTGGTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (20 bp):
TAAGTAAATGAAATGAAAAG
Found at i:55559322 original size:2 final size:2
Alignment explanation
Indices: 55559315--55559345 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55559305 TACAAATGTG
55559315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55559346 GGAAATGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55569801 original size:43 final size:43
Alignment explanation
Indices: 55569676--55569838 Score: 167
Period size: 43 Copynumber: 3.8 Consensus size: 43
55569666 CAGAAAACTC
* *
55569676 ATACAATGCCAACGTCCCAGACGTGGTCTTACATAT-AATCAA
1 ATACAATGCCAACATCCCAGACGTGGTCTTACACATAAATCAA
*
55569718 ATATCAATACC-ACTATCCCAGACAG-GGTCTT--ACATGAAATCAA
1 ATA-CAATGCCAAC-ATCCCAGAC-GTGGTCTTACACAT-AAATCAA
* *
55569761 ATACGATGCCAACATCCTAGACGTGGTCTTACACATAAATCATA
1 ATACAATGCCAACATCCCAGACGTGGTCTTACACATAAATCA-A
* *
55569805 AGT-CGATGCCAACGTCCCAGACGTGGTCTTACAC
1 A-TACAATGCCAACATCCCAGACGTGGTCTTACAC
55569839 GAAAACACAT
Statistics
Matches: 102, Mismatches: 8, Indels: 20
0.78 0.06 0.15
Matches are distributed among these distances:
41 4 0.04
42 24 0.24
43 37 0.36
44 36 0.35
45 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.23
Consensus pattern (43 bp):
ATACAATGCCAACATCCCAGACGTGGTCTTACACATAAATCAA
Found at i:55569816 original size:44 final size:42
Alignment explanation
Indices: 55569681--55569838 Score: 155
Period size: 44 Copynumber: 3.7 Consensus size: 42
55569671 AACTCATACA
* * *
55569681 ATGCCAACGTCCCAGACGTGGTCTTACATAT-AATCAAATATCA
1 ATGCCAACATCCCAGACGTGGTCTTACACATAAATC-AA-ATCG
*
55569724 ATACC-ACTATCCCAGACAG-GGTCTT--ACATGAAATCAAATACG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACAT-AAATCAAAT-CG
*
55569766 ATGCCAACATCCTAGACGTGGTCTTACACATAAATCATAAGTCG
1 ATGCCAACATCCCAGACGTGGTCTTACACATAAATCA-AA-TCG
*
55569810 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACATCCCAGACGTGGTCTTACAC
55569839 GAAAACACAT
Statistics
Matches: 96, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
41 6 0.06
42 23 0.24
43 30 0.31
44 36 0.38
45 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (42 bp):
ATGCCAACATCCCAGACGTGGTCTTACACATAAATCAAATCG
Found at i:55580197 original size:45 final size:45
Alignment explanation
Indices: 55580059--55580231 Score: 163
Period size: 45 Copynumber: 3.8 Consensus size: 45
55580049 ACCATCAAAG
* * * * * * **
55580059 GATGTCATAGTGTGTCTCAGCTATGGTATTAATCCTTTTTACCAT
1 GATGTCATAGTGTCTTTCAGCTATGGTCTTACTCATTTATGTCAT
* *
55580104 GAT-TCCATAGTGTCTTTTAG-TCATTGTCTTACTCATTTATGTCAT
1 GATGT-CATAGTGTCTTTCAGCT-ATGGTCTTACTCATTTATGTCAT
* *
55580149 GATGTGATAGTGTCTTTCAGCTATGGTCTTACTCATCTT-TGTCCT
1 GATGTCATAGTGTCTTTCAGCTATGGTCTTACTCAT-TTATGTCAT
** *
55580194 GATGTCATAGCATCTTTCAGCTATGGTCATACTCATTT
1 GATGTCATAGTGTCTTTCAGCTATGGTCTTACTCATTT
55580232 TAGGTGTATA
Statistics
Matches: 105, Mismatches: 18, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
44 4 0.04
45 97 0.92
46 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.44
Consensus pattern (45 bp):
GATGTCATAGTGTCTTTCAGCTATGGTCTTACTCATTTATGTCAT
Found at i:55580222 original size:22 final size:23
Alignment explanation
Indices: 55580161--55580225 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
55580151 TGTGATAGTG
* *
55580161 TCTTTCAGCTATGGTCTTACTCA
1 TCTTTCAGCTATGGTCATACGCA
***
55580184 TCTTTGTCCTGAT-GTCATA-GCA
1 TCTTTCAGCT-ATGGTCATACGCA
55580206 TCTTTCAGCTATGGTCATAC
1 TCTTTCAGCTATGGTCATAC
55580226 TCATTTTAGG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
21 2 0.06
22 15 0.48
23 12 0.39
24 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (23 bp):
TCTTTCAGCTATGGTCATACGCA
Found at i:55582592 original size:40 final size:40
Alignment explanation
Indices: 55582532--55582735 Score: 225
Period size: 40 Copynumber: 5.1 Consensus size: 40
55582522 CGGGATTCAA
* ** *
55582532 CCGGATATAACCACAAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGC
* *** *
55582572 CCGGATTTGGTAACTTGCAC-AATTGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGC
55582612 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
55582652 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
* * ** * *
55582692 CTGGATATAATC-ACTAGCATAAATGCCTTCGAGACTTAGC
1 CCGGATATAA-CAACTCGCACGAATGCCTTCGGGTCTTAGC
55582732 CCGG
1 CCGG
55582736 GTATCATTCA
Statistics
Matches: 142, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 139 0.98
41 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:55587112 original size:39 final size:40
Alignment explanation
Indices: 55587012--55587193 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
55587002 TCGAATGATG
* * *
55587012 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
55587052 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
*
55587092 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * *
55587131 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
55587172 -CC-GGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
55587194 TGAGTGAGTC
Statistics
Matches: 117, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
39 50 0.43
40 58 0.50
41 9 0.08
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:55587186 original size:79 final size:81
Alignment explanation
Indices: 55587012--55587195 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
55587002 TCGAATGATG
* * *
55587012 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
55587076 CGTGCGAGTTAATAAA
66 CGTGCGAGTCAATAAA
* **
55587092 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
55587154 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATA-AA
**
55587172 -CC-GGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55587196 AGTGAGTCGT
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 6 0.07
79 64 0.71
80 20 0.22
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATAAA
Found at i:55588616 original size:46 final size:45
Alignment explanation
Indices: 55588566--55588736 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 45
55588556 TGGTTGAGCA
*
55588566 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTTATGGATGCAAACG
* * * *
55588612 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCCTTATGGATGCAA--A--CG
*
55588659 TCCGAACTCGTTGAGTTGAGTCCGAGTT-CTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCCTTATGGATGCAAACG
* *
55588703 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTTA
55588737 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
44 27 0.26
45 3 0.03
46 36 0.34
47 28 0.27
48 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCCTTATGGATGCAAACG
Found at i:55588729 original size:91 final size:92
Alignment explanation
Indices: 55588563--55588731 Score: 286
Period size: 91 Copynumber: 1.8 Consensus size: 92
55588553 GGATGGTTGA
* *
55588563 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTT-ACTTATGGATGCAAACGCCCGAACTCGTTGAGT
55588628 TGAGTCCGAGTTCGTGAGATGTAACTAG
65 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
55588656 GCATCCGAACTCGTTGAGTTGAGTCCGAGTT-CTTATGGATGCGAACGCCCGAGCTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTACTTATGGATGCAAACGCCCGAACTCGTTGAGTT
55588720 GAGTCCGAGTTC
66 GAGTCCGAGTTC
55588732 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
91 41 0.57
93 31 0.43
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTACTTATGGATGCAAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:55596074 original size:46 final size:46
Alignment explanation
Indices: 55596024--55596195 Score: 208
Period size: 45 Copynumber: 3.7 Consensus size: 46
55596014 TGGTTGAGCA
*
55596024 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
55596070 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
55596117 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
55596163 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
55596196 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 6 0.06
45 34 0.32
46 30 0.28
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:55596457 original size:19 final size:20
Alignment explanation
Indices: 55596420--55596457 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
55596410 ATAAGGTGGT
55596420 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
55596440 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
55596458 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:55597267 original size:28 final size:28
Alignment explanation
Indices: 55597227--55597280 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
55597217 AGGCGTTACA
*
55597227 TGATTCGTACAAATTTATCCTTCAAATT
1 TGATTCGTACAAATTCATCCTTCAAATT
55597255 TGATTCGTACAAATTCATCCTTCAAA
1 TGATTCGTACAAATTCATCCTTCAAA
55597281 GTGATTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.39
Consensus pattern (28 bp):
TGATTCGTACAAATTCATCCTTCAAATT
Found at i:55597269 original size:15 final size:15
Alignment explanation
Indices: 55597227--55597269 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
55597217 AGGCGTTACA
55597227 TGATTCGTACAAATT
1 TGATTCGTACAAATT
* *
55597242 T-A-TCCTTCAAATT
1 TGATTCGTACAAATT
55597255 TGATTCGTACAAATT
1 TGATTCGTACAAATT
55597270 CATCCTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 10 0.45
14 2 0.09
15 10 0.45
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (15 bp):
TGATTCGTACAAATT
Found at i:55599833 original size:27 final size:26
Alignment explanation
Indices: 55599786--55599836 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
55599776 CGAGGCTGCC
*
55599786 AGATATTGTGACGAAGTCACCAGAAT
1 AGATATTGTGACGAAGCCACCAGAAT
* *
55599812 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
55599837 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAT
Found at i:55600519 original size:27 final size:27
Alignment explanation
Indices: 55600489--55600607 Score: 148
Period size: 27 Copynumber: 4.4 Consensus size: 27
55600479 GAGGCAAAAT
* * *
55600489 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
55600516 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
55600543 GTTATTTCTACCCTACAAAGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
55600570 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
55600597 AGTAATTCTAC
1 GGTAATTCTAC
55600608 AACTTATCCA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:55600606 original size:54 final size:53
Alignment explanation
Indices: 55600490--55600607 Score: 164
Period size: 54 Copynumber: 2.2 Consensus size: 53
55600480 AGGCAAAATG
* *
55600490 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTC
1 GTAATTCTACCCCACAAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTC
* * * *
55600543 GTTATTTCTACCCTACAAAGGTATTTCGGTAATTCTACCTTACAGGGGTATTTC
1 G-TAATTCTACCCCACAAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTC
55600597 AGTAATTCTAC
1 -GTAATTCTAC
55600608 AACTTATCCA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
53 1 0.02
54 54 0.96
55 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (53 bp):
GTAATTCTACCCCACAAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTC
Found at i:55605498 original size:23 final size:23
Alignment explanation
Indices: 55605456--55605502 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
55605446 TTTGGTGTGA
**
55605456 TAGTTGTGGATATTTAGGATTGT
1 TAGTTGTGGATACCTAGGATTGT
*
55605479 TAGTTGTGGATACCTGGGATTGT
1 TAGTTGTGGATACCTAGGATTGT
55605502 T
1 T
55605503 TGTATGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.04, G:0.32, T:0.45
Consensus pattern (23 bp):
TAGTTGTGGATACCTAGGATTGT
Found at i:55607693 original size:28 final size:28
Alignment explanation
Indices: 55607636--55607697 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
55607626 TGGGAAGTAG
* *
55607636 TTGGGCCTGATGGGCCATATGAATATGA
1 TTGGGCCTAATGGGCCATATGAAGATGA
*
55607664 TTGGGCCTAATGGGCCATGTGAACGA-GA
1 TTGGGCCTAATGGGCCATATGAA-GATGA
55607692 TTGGGC
1 TTGGGC
55607698 TTAAAGGGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATGAAGATGA
Found at i:55608045 original size:27 final size:27
Alignment explanation
Indices: 55608015--55608300 Score: 151
Period size: 27 Copynumber: 10.6 Consensus size: 27
55608005 TAATAAAGAG
*
55608015 AAATTACCGAAATACCCCCGAATTGTA
1 AAATTATCGAAATACCCCCGAATTGTA
* * *
55608042 AAATTATCGAAGTA-CCCCTAGTTTGTA
1 AAATTATCGAAATACCCCCGA-ATTGTA
* *
55608069 AAATTATCGAAGTACCCCC-AGTTTGTA
1 AAATTATCGAAATACCCCCGA-ATTGTA
* ** *
55608096 AAATTATTG-AATACCTTC-AGTTCGTA
1 AAATTATCGAAATACCCCCGAATT-GTA
* *
55608122 AAATTACCGAAATA-CCCCAAATTTGTA
1 AAATTATCGAAATACCCCCGAA-TTGTA
* * ***
55608149 AAATTACCAAAATA-CCTTAAATTTGTA
1 AAATTATCGAAATACCCCCGAA-TTGTA
* **
55608176 AAATTA-CCAAA-ACACCCTTAATTTGTA
1 AAATTATCGAAATAC-CCCCGAA-TTGTA
* * *
55608203 AAATTATCGAAACACCCTCGATTTGTA
1 AAATTATCGAAATACCCCCGAATTGTA
* **
55608230 AAATTA-CTAAAATACCCTAG-ATATGTA
1 AAATTATC-GAAATACCCCCGAAT-TGTA
* * *
55608257 AAATTATCAAAACACCCCCGATTTGATA
1 AAATTATCGAAATACCCCCGAATTG-TA
55608285 AAATTATCGAAATACC
1 AAATTATCGAAATACC
55608301 TTTACAGTGT
Statistics
Matches: 209, Mismatches: 35, Indels: 29
0.77 0.13 0.11
Matches are distributed among these distances:
25 3 0.01
26 30 0.14
27 143 0.68
28 31 0.15
29 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.29
Consensus pattern (27 bp):
AAATTATCGAAATACCCCCGAATTGTA
Found at i:55608182 original size:54 final size:54
Alignment explanation
Indices: 55608015--55608300 Score: 236
Period size: 54 Copynumber: 5.3 Consensus size: 54
55608005 TAATAAAGAG
* * * *
55608015 AAATTACCGAAATACCCCCGAA-TTGTAAAATTATCGAAGTACCC-CTAGTTTGTA
1 AAATTACCGAAATA-CCCCAAATTTGTAAAATTATCAAAATACCCTC-AATTTGTA
* * * * ** * * *
55608069 AAATTATCGAAGTACCCCCAGTTTGTAAAATTAT-TGAATACCTTCAGTTCGTA
1 AAATTACCGAAATACCCCAAATTTGTAAAATTATCAAAATACCCTCAATTTGTA
* * *
55608122 AAATTACCGAAATACCCCAAATTTGTAAAATTACCAAAATACCTTAAATTTGTA
1 AAATTACCGAAATACCCCAAATTTGTAAAATTATCAAAATACCCTCAATTTGTA
* * ** * * *
55608176 AAATTACCAAAACACCCTTAATTTGTAAAATTATCGAAACACCCTCGATTTGTA
1 AAATTACCGAAATACCCCAAATTTGTAAAATTATCAAAATACCCTCAATTTGTA
** * * * * * *
55608230 AAATTACTAAAATACCCTAGATATGTAAAATTATCAAAACACCCCCGATTTGATA
1 AAATTACCGAAATACCCCAAATTTGTAAAATTATCAAAATACCCTCAATTTG-TA
*
55608285 AAATTATCGAAATACC
1 AAATTACCGAAATACC
55608301 TTTACAGTGT
Statistics
Matches: 189, Mismatches: 39, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
53 46 0.24
54 128 0.68
55 15 0.08
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.29
Consensus pattern (54 bp):
AAATTACCGAAATACCCCAAATTTGTAAAATTATCAAAATACCCTCAATTTGTA
Found at i:55608232 original size:81 final size:81
Alignment explanation
Indices: 55608119--55608296 Score: 232
Period size: 81 Copynumber: 2.2 Consensus size: 81
55608109 CCTTCAGTTC
* * * *
55608119 GTAAAATTACCGAAATACCCCAAATTTGTAAAATTACCAAAATACCTTAAATTTGTAAAATTACC
1 GTAAAATTATCGAAACACCCCAAATTTGTAAAATTACCAAAATACCCTAAATATGTAAAATTACC
**
55608184 AAAACACCCTTAATTT
66 AAAACACCCCCAATTT
* * * *
55608200 GTAAAATTATCGAAACACCCTC-GATTTGTAAAATTACTAAAATACCCTAGATATGTAAAATTAT
1 GTAAAATTATCGAAACACCC-CAAATTTGTAAAATTACCAAAATACCCTAAATATGTAAAATTAC
*
55608264 CAAAACACCCCCGATTT
65 CAAAACACCCCCAATTT
55608281 GATAAAATTATCGAAA
1 G-TAAAATTATCGAAA
55608297 TACCTTTACA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
81 69 0.82
82 15 0.18
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (81 bp):
GTAAAATTATCGAAACACCCCAAATTTGTAAAATTACCAAAATACCCTAAATATGTAAAATTACC
AAAACACCCCCAATTT
Found at i:55612075 original size:49 final size:49
Alignment explanation
Indices: 55611994--55612153 Score: 252
Period size: 49 Copynumber: 3.3 Consensus size: 49
55611984 CCCTTCGGGA
* * * * * *
55611994 CTTATCACAT-T-TATACACTTCCACATCCATCACGTTGGCCACTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55612041 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55612090 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
55612139 CTTATCACATATATA
1 CTTATCACATATATA
55612154 TATCTCATAC
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
47 10 0.10
48 1 0.01
49 94 0.90
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55619763 original size:40 final size:40
Alignment explanation
Indices: 55619669--55619813 Score: 202
Period size: 40 Copynumber: 3.6 Consensus size: 40
55619659 TACTCGAATG
*
55619669 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
55619710 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
55619750 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
*
55619790 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
55619814 CTTGTGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 63 0.68
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:55627777 original size:40 final size:40
Alignment explanation
Indices: 55627683--55627827 Score: 202
Period size: 40 Copynumber: 3.6 Consensus size: 40
55627673 TACTCGAATG
*
55627683 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
55627724 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
55627764 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
*
55627804 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
55627828 CTTGTGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 63 0.68
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:55633872 original size:64 final size:64
Alignment explanation
Indices: 55633794--55633934 Score: 201
Period size: 64 Copynumber: 2.2 Consensus size: 64
55633784 TTGGTATCGA
* * * *
55633794 GGTAAGTTCGTATGCGAGTAATGCAATATGTAATATATTTTAAATGCTTAAATATTGCACGTAT
1 GGTAAGTTCATATGCAAATAATGCAATATGTAACATATTTTAAATGCTTAAATATTGCACGTAT
* * * *
55633858 GGTAAGTTCATATGCAAATTATGCAATATGTACCATATTTTAAATGCTTTAATATTGCATGTAT
1 GGTAAGTTCATATGCAAATAATGCAATATGTAACATATTTTAAATGCTTAAATATTGCACGTAT
*
55633922 GGTAAGTACATAT
1 GGTAAGTTCATAT
55633935 ATAATTAATG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (64 bp):
GGTAAGTTCATATGCAAATAATGCAATATGTAACATATTTTAAATGCTTAAATATTGCACGTAT
Found at i:55634160 original size:22 final size:22
Alignment explanation
Indices: 55634135--55634176 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55634125 TACTAGGGAC
55634135 TATGCAATCTGAGCTCATGAGT
1 TATGCAATCTGAGCTCATGAGT
***
55634157 TATGTGGTCTGAGCTCATGA
1 TATGCAATCTGAGCTCATGA
55634177 TATATGTGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (22 bp):
TATGCAATCTGAGCTCATGAGT
Found at i:55634182 original size:22 final size:22
Alignment explanation
Indices: 55634142--55634184 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55634132 GACTATGCAA
55634142 TCTGAGCTCATGAGTTATGTGG
1 TCTGAGCTCATGAGTTATGTGG
55634164 TCTGAGCTCATGA-TATATGTG
1 TCTGAGCTCATGAGT-TATGTG
55634185 ACACATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (22 bp):
TCTGAGCTCATGAGTTATGTGG
Found at i:55635767 original size:40 final size:40
Alignment explanation
Indices: 55635712--55635792 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
55635702 GAGTCTATTT
55635712 TTGGAAAAATCAAGCGGATCTTAATTTATAGTTCACTAAC
1 TTGGAAAAATCAAGCGGATCTTAATTTATAGTTCACTAAC
55635752 TTGGAAAAATCAAGCGGATCTTAATTTATAGTTCACTAAC
1 TTGGAAAAATCAAGCGGATCTTAATTTATAGTTCACTAAC
55635792 T
1 T
55635793 CAAGATATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (40 bp):
TTGGAAAAATCAAGCGGATCTTAATTTATAGTTCACTAAC
Found at i:55637521 original size:28 final size:29
Alignment explanation
Indices: 55637411--55637521 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
55637401 GTGAGCATGA
* * *
55637411 ATATGAATGTGA-CTGGGCCTAACGAGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
55637439 ACATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
55637468 ATAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* *
55637497 ATATGAATATGA-TTGGGCTTAATGG
1 ATATGAATGTGATTTGGGCCTAATGG
55637522 ACAAGAAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.33
29 46 0.66
30 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:55640458 original size:7 final size:7
Alignment explanation
Indices: 55640446--55640471 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55640436 CCTAGATGAA
55640446 TTGGGCT
1 TTGGGCT
55640453 TTGGGCT
1 TTGGGCT
55640460 TTGGGCT
1 TTGGGCT
55640467 TTGGG
1 TTGGG
55640472 TTTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.46, T:0.42
Consensus pattern (7 bp):
TTGGGCT
Found at i:55641644 original size:8 final size:8
Alignment explanation
Indices: 55641622--55641681 Score: 68
Period size: 8 Copynumber: 7.6 Consensus size: 8
55641612 TATGAATCGG
55641622 CGAAA-GC
1 CGAAATGC
*
55641629 CAAAATGC
1 CGAAATGC
55641637 CGAAATGC
1 CGAAATGC
*
55641645 CAAAATGC
1 CGAAATGC
*
55641653 CAAAATGC
1 CGAAATGC
*
55641661 TGAAATGC
1 CGAAATGC
55641669 CGAAATGC
1 CGAAATGC
*
55641677 AGAAA
1 CGAAA
55641682 AGCCAAAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
7 4 0.09
8 41 0.91
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (8 bp):
CGAAATGC
Found at i:55641648 original size:16 final size:16
Alignment explanation
Indices: 55641622--55641676 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
55641612 TATGAATCGG
55641622 CGAAA-GCCAAAATGC
1 CGAAATGCCAAAATGC
55641637 CGAAATGCCAAAATGC
1 CGAAATGCCAAAATGC
* **
55641653 CAAAATGCTGAAATGC
1 CGAAATGCCAAAATGC
55641669 CGAAATGC
1 CGAAATGC
55641677 AGAAAAGCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
15 5 0.14
16 30 0.86
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.13
Consensus pattern (16 bp):
CGAAATGCCAAAATGC
Found at i:55641659 original size:24 final size:24
Alignment explanation
Indices: 55641627--55641676 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
55641617 ATCGGCGAAA
55641627 GCCAAAATGCCGAAATGCCAAAAT
1 GCCAAAATGCCGAAATGCCAAAAT
* *
55641651 GCCAAAATGCTGAAATGCCGAAAT
1 GCCAAAATGCCGAAATGCCAAAAT
55641675 GC
1 GC
55641677 AGAAAAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (24 bp):
GCCAAAATGCCGAAATGCCAAAAT
Found at i:55641945 original size:29 final size:29
Alignment explanation
Indices: 55641912--55642013 Score: 107
Period size: 29 Copynumber: 3.6 Consensus size: 29
55641902 ATGAAATGAC
**
55641912 TGGGCCTAACAGGCCATATAAATGTGAAT
1 TGGGCCTAATGGGCCATATAAATGTGAAT
* * * *
55641941 TGGGCCTAATGGGCAATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGAAT
* * *
55641970 TTGGCCTAATGGGCCATATGAATATG-AT
1 TGGGCCTAATGGGCCATATAAATGTGAAT
*
55641998 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
55642014 GATACAAGTA
Statistics
Matches: 58, Mismatches: 15, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
28 15 0.26
29 43 0.74
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGAAT
Found at i:55642012 original size:28 final size:28
Alignment explanation
Indices: 55641900--55642013 Score: 97
Period size: 29 Copynumber: 4.0 Consensus size: 28
55641890 GTGAGCATGA
* **
55641900 ATATGAA-ATGACTGGGCCTAACAGGCC
1 ATATGAATATGATTGGGCCTAATGGGCC
* * *
55641927 ATATAAATGTGAATTGGGCCTAATGGGCA
1 ATATGAATATG-ATTGGGCCTAATGGGCC
** *
55641956 ATAT-ACAGGTGATTTTGGCCTAATGGGCC
1 ATATGA-ATATGA-TTGGGCCTAATGGGCC
*
55641985 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATATGATTGGGCCTAATGGGCC
55642013 A
1 A
55642014 GATACAAGTA
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
27 6 0.09
28 19 0.28
29 43 0.62
30 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (28 bp):
ATATGAATATGATTGGGCCTAATGGGCC
Found at i:55648010 original size:12 final size:12
Alignment explanation
Indices: 55647993--55648020 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
55647983 TCACATGCCT
55647993 GTGTGCTAGGCC
1 GTGTGCTAGGCC
55648005 GTGTGCTAGGCC
1 GTGTGCTAGGCC
55648017 GTGT
1 GTGT
55648021 AACAGCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.21, G:0.43, T:0.29
Consensus pattern (12 bp):
GTGTGCTAGGCC
Found at i:55648406 original size:22 final size:22
Alignment explanation
Indices: 55648380--55648424 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
55648370 ATTATGTGTA
*
55648380 TTAATTCATAATTCAA-TTAATT
1 TTAATT-ATAATCCAATTTAATT
*
55648402 TTAATTTTAATCCAATTTAATT
1 TTAATTATAATCCAATTTAATT
55648424 T
1 T
55648425 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTATAATCCAATTTAATT
Found at i:55649200 original size:15 final size:15
Alignment explanation
Indices: 55649180--55649209 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55649170 TGTTATAGGC
55649180 CTCGGTAAGATGTTT
1 CTCGGTAAGATGTTT
55649195 CTCGGTAAGATGTTT
1 CTCGGTAAGATGTTT
55649210 GACTAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (15 bp):
CTCGGTAAGATGTTT
Found at i:55651179 original size:48 final size:48
Alignment explanation
Indices: 55651106--55651225 Score: 152
Period size: 48 Copynumber: 2.5 Consensus size: 48
55651096 GTCATTAGGG
* *
55651106 GATTCATTTATTTGGCTTCAGGCCATAATATTGGAACTTTGGGTGAGA
1 GATTCATTGATTTGGCTTCAGGCCATAATATTAGAACTTTGGGTGAGA
* * * *
55651154 GCTTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTTGGGTGTGA
1 GATTCATTGATTTGGCTTCAGGCCATAATATTAGAACTTTGGGTGAGA
* *
55651202 GATAT-ATTGAGTTGGCTTCGGGCC
1 GAT-TCATTGATTTGGCTTCAGGCC
55651226 TTGACATTGG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 61 0.98
49 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.37
Consensus pattern (48 bp):
GATTCATTGATTTGGCTTCAGGCCATAATATTAGAACTTTGGGTGAGA
Found at i:55658223 original size:34 final size:34
Alignment explanation
Indices: 55658180--55658259 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 34
55658170 TTTCTATTGG
* **
55658180 ACATTGATACTGTTACTATTATGGTTTAAGGTCC
1 ACATTGATACTGTTACTACTATGGGCTAAGGTCC
* *
55658214 ACATTGATACTATTACTGCTATGGGCTAAGGTCC
1 ACATTGATACTGTTACTACTATGGGCTAAGGTCC
* *
55658248 TCACTGATACTG
1 ACATTGATACTG
55658260 GACTTATAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (34 bp):
ACATTGATACTGTTACTACTATGGGCTAAGGTCC
Found at i:55659061 original size:22 final size:22
Alignment explanation
Indices: 55659031--55659073 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
55659021 CGCCATAGAC
*
55659031 AGGATAGCACATAGCCGTAAAT
1 AGGACAGCACATAGCCGTAAAT
*
55659053 AGGACAGCACATAGTCGTAAA
1 AGGACAGCACATAGCCGTAAA
55659074 CATCGCAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (22 bp):
AGGACAGCACATAGCCGTAAAT
Found at i:55659281 original size:27 final size:27
Alignment explanation
Indices: 55659251--55659312 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
55659241 TAATCATATA
* *
55659251 TTGGCACATAGCCTTAGGAAAATACAT
1 TTGGCACAAAGCCTTAGGAAAAAACAT
55659278 TTGGCACAAAGCCTTAGGAAAAAACAT
1 TTGGCACAAAGCCTTAGGAAAAAACAT
55659305 TTGGCACA
1 TTGGCACA
55659313 CTGCCATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (27 bp):
TTGGCACAAAGCCTTAGGAAAAAACAT
Found at i:55659340 original size:22 final size:22
Alignment explanation
Indices: 55659315--55659369 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
55659305 TTGGCACACT
*
55659315 GCCATAATCAGGTTGCCACAGA
1 GCCATAATCAGGTTGCCACAAA
* *
55659337 GCCAT-ATGTAGGTTGGCACAAA
1 GCCATAAT-CAGGTTGCCACAAA
55659359 GCCATAATCAG
1 GCCATAATCAG
55659370 AATAATTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 23 0.85
23 2 0.07
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (22 bp):
GCCATAATCAGGTTGCCACAAA
Found at i:55659573 original size:41 final size:41
Alignment explanation
Indices: 55659512--55659633 Score: 181
Period size: 41 Copynumber: 3.0 Consensus size: 41
55659502 AAAAGCCATT
* * * *
55659512 GGTGGATCCAAGGTCGTCAAGAAACCATGCAATCCTTAATC
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATC
* *
55659553 GGTGGATCCACGGTCATCAAGCAACCATTCGATCCTCAATC
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATC
*
55659594 GGTAGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
55659634 TTCTTCCTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (41 bp):
GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATC
Found at i:55659923 original size:27 final size:27
Alignment explanation
Indices: 55659893--55660178 Score: 200
Period size: 27 Copynumber: 10.6 Consensus size: 27
55659883 GGTAAATATA
*
55659893 CAAACCAAGGGTATTTCGGTAATTTTC
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * *
55659920 CAAACCAATGGTATTTCTGTAATTTTT
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * ** * *
55659947 AAAAGTCAAGGGTATTTCTATATTTTTC
1 CAAA-CCAAGGGTATTTCGGTAATTTTG
* *
55659975 CAAATCAAGGGTATTTCGGTAATTTTC
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * * **
55660002 CAAATC-AGGGATCTTTTGGTAATTTAA
1 CAAACCAAGGG-TATTTCGGTAATTTTG
* * * *
55660029 AAAACCAGGGGTATTTTGGTAATTTTA
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * * *
55660056 CAAA-CTAGGGTGTTTTGGTAGTTTTG
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * * *
55660082 CTAATCGAGGGTATTTTGGTAATTTTG
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * *
55660109 TAAATCAAGGGTATTT-AGTAATTTTG
1 CAAACCAAGGGTATTTCGGTAATTTTG
* * *
55660135 TAAACCAAGGGCATTTCAGTAATTTTG
1 CAAACCAAGGGTATTTCGGTAATTTTG
* *
55660162 TAAACCAAGGGCATTTC
1 CAAACCAAGGGTATTTC
55660179 AATAATTCTA
Statistics
Matches: 216, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
26 47 0.22
27 145 0.67
28 24 0.11
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (27 bp):
CAAACCAAGGGTATTTCGGTAATTTTG
Found at i:55660134 original size:53 final size:52
Alignment explanation
Indices: 55659871--55660177 Score: 140
Period size: 53 Copynumber: 5.7 Consensus size: 52
55659861 TTTCACCCTA
* * * ** * **
55659871 CAAGGGTGTTTTGGTAAATATACAAACCAAGGGTATTTCGGTAATTTTCCAAAC
1 CAAGGGTATTTTGGTAATTTTGTAAA-CAAGGGTATTT-AGTAATTTTGTAAAC
* * *
55659925 CAATGGTATTTCT-GTAATTTT-TAAAAGTCAAGGGTATTT-CTATATTTT-TCCAAAT
1 CAAGGGTATTT-TGGTAATTTTGT-AAA--CAAGGGTATTTAGTA-ATTTTGT--AAAC
* ** * * ***
55659980 CAAGGGTATTTCGGTAATTTTCCAAATC-AGGGATCTTTTGGTAATTTAAAAAAC
1 CAAGGGTATTTTGGTAATTTTGTAAA-CAAGGG-T-ATTTAGTAATTTTGTAAAC
* ** * * * * *
55660034 CAGGGGTATTTTGGTAATTTTACAAACTAGGGTGTTTTGGTAGTTTTGCT-AAT
1 CAAGGGTATTTTGGTAATTTTGTAAACAAGGGT-ATTTAGTAATTTTG-TAAAC
*
55660087 CGAGGGTATTTTGGTAATTTTGTAAATCAAGGGTATTTAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTGTAAA-CAAGGGTATTTAGTAATTTTGTAAAC
* ** *
55660140 CAAGGGCATTTCAGTAATTTTGTAAACCAAGGGCATTT
1 CAAGGGTATTTTGGTAATTTTGTAAA-CAAGGGTATTT
55660178 CAATAATTCT
Statistics
Matches: 196, Mismatches: 41, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
52 1 0.01
53 88 0.45
54 62 0.32
55 43 0.22
56 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (52 bp):
CAAGGGTATTTTGGTAATTTTGTAAACAAGGGTATTTAGTAATTTTGTAAAC
Found at i:55660224 original size:26 final size:27
Alignment explanation
Indices: 55660172--55660249 Score: 104
Period size: 26 Copynumber: 2.9 Consensus size: 27
55660162 TAAACCAAGG
* *
55660172 GCATTTCAATAATTCTACCCTATAGGA
1 GCATTTCAGTAATTCTACCCTACAGGA
55660199 GCATTTCAGTAATT-TACCCTACAGGA
1 GCATTTCAGTAATTCTACCCTACAGGA
* * *
55660225 GTATTTCAGTAATACTAGCCTACAG
1 GCATTTCAGTAATTCTACCCTACAG
55660250 ATATGAGATT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 23 0.51
27 22 0.49
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (27 bp):
GCATTTCAGTAATTCTACCCTACAGGA
Found at i:55666946 original size:22 final size:21
Alignment explanation
Indices: 55666895--55666946 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
55666885 GCCTCCAGCG
**
55666895 CGGGCGTGTCCTAGGGTCACA
1 CGGGCGTGTCCTAGGACCACA
* * *
55666916 CGAGTGTGTCCCTTGGACCACA
1 CGGGCGTGT-CCTAGGACCACA
55666938 CGGGCGTGT
1 CGGGCGTGT
55666947 AAGCCCTGCA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.13, C:0.29, G:0.37, T:0.21
Consensus pattern (21 bp):
CGGGCGTGTCCTAGGACCACA
Found at i:55673546 original size:22 final size:22
Alignment explanation
Indices: 55673499--55673565 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
55673489 TGGCCTCCAG
* **
55673499 CACGGGCATGT-CCTAGGGTCA
1 CACGGGCATGTGCCTTGGACCA
*
55673520 CACGGGC-TCTTGCCTTGGACCA
1 CACGGGCAT-GTGCCTTGGACCA
55673542 CACGGGCATGTGCCTTGGACCA
1 CACGGGCATGTGCCTTGGACCA
55673564 CA
1 CA
55673566 TAGGCGTGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 8 0.21
22 28 0.74
23 1 0.03
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.19
Consensus pattern (22 bp):
CACGGGCATGTGCCTTGGACCA
Found at i:55673575 original size:22 final size:22
Alignment explanation
Indices: 55673530--55673575 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
55673520 CACGGGCTCT
*
55673530 TGCCTTGGACCACACGGGCATG
1 TGCCTTGGACCACACAGGCATG
* *
55673552 TGCCTTGGACCACATAGGCGTG
1 TGCCTTGGACCACACAGGCATG
55673574 TG
1 TG
55673576 AGCCCTGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (22 bp):
TGCCTTGGACCACACAGGCATG
Found at i:55675664 original size:59 final size:60
Alignment explanation
Indices: 55675593--55675709 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 60
55675583 ATCACTTTAA
* * *
55675593 TATTAAATTAATATAATATTTATC-AAGATAAATATTAAATTAAATTTAATATTAAATTT
1 TATTAAAATAATAGAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATTT
*
55675652 TATTAAAATAATAGAATATTTATCTTGCAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTATC-T-AAGATAAACATTAAATTAAATTTAATATTAA
55675710 GATAATCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.43
62 29 0.57
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (60 bp):
TATTAAAATAATAGAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATTT
Found at i:55675735 original size:20 final size:18
Alignment explanation
Indices: 55675688--55675736 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
55675678 GCAGATAAAC
55675688 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
55675705 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
55675725 ATTAAATTAATA
1 ATTAAATTAATA
55675737 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:55678445 original size:18 final size:18
Alignment explanation
Indices: 55678422--55678456 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55678412 GATCAAGTAA
*
55678422 AATTAAATTAATCTAATT
1 AATTAAATTAATATAATT
55678440 AATTAAATTAATATAAT
1 AATTAAATTAATATAAT
55678457 ATTTTCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAAATTAATATAATT
Found at i:55678868 original size:12 final size:12
Alignment explanation
Indices: 55678849--55678947 Score: 52
Period size: 12 Copynumber: 8.6 Consensus size: 12
55678839 TTATTTTAAT
55678849 ATATTTAATATTA
1 ATATTTAAT-TTA
55678862 A-ATTTAATTTA
1 ATATTTAATTTA
55678873 ATATTT-ATCTTA
1 ATATTTAAT-TTA
*
55678885 ATA-GT-ATTT-
1 ATATTTAATTTA
55678894 -TA-TTAATTTA
1 ATATTTAATTTA
* * *
55678904 ATATTAAAGTGA
1 ATATTTAATTTA
*
55678916 TTATCTTAATATTA
1 ATAT-TTAAT-TTA
55678930 A-ATTTAATTTA
1 ATATTTAATTTA
*
55678941 ATGTTTA
1 ATATTTA
55678948 TCTTATAGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
8 3 0.05
9 4 0.06
10 2 0.03
11 15 0.23
12 34 0.52
13 6 0.09
14 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (12 bp):
ATATTTAATTTA
Found at i:55678885 original size:17 final size:16
Alignment explanation
Indices: 55678851--55678908 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
55678841 ATTTTAATAT
*
55678851 ATTTAATATTAAATTTA
1 ATTTAATATT-TATTTA
55678868 ATTTAATATTTATCTTA
1 ATTTAATATTTAT-TTA
*
55678885 A--TAGTATTT-TATTA
1 ATTTAATATTTAT-TTA
55678899 ATTTAATATT
1 ATTTAATATT
55678909 AAAGTGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 8 0.24
17 14 0.41
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTAATATTTATTTA
Found at i:55678929 original size:68 final size:72
Alignment explanation
Indices: 55678853--55678990 Score: 212
Period size: 72 Copynumber: 2.0 Consensus size: 72
55678843 TTTAATATAT
* **
55678853 TTAATATTAAATTTAATTTAATATTTATC-T-TA-AT-AGTATTTTATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATATTTATCTTATAGATAAGTATTCTATTAATTTAATAACAAAGT
55678914 GATTATC
66 GATTATC
*
55678921 TTAATATTAAATTTAATTTAATGTTTATCTTATAGATAAGTATTCTATTAATTTAATAACAAAGT
1 TTAATATTAAATTTAATTTAATATTTATCTTATAGATAAGTATTCTATTAATTTAATAACAAAGT
55678986 GATTA
66 GATTA
55678991 AGTTTAATCA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
68 28 0.45
69 1 0.02
70 2 0.03
71 2 0.03
72 29 0.47
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (72 bp):
TTAATATTAAATTTAATTTAATATTTATCTTATAGATAAGTATTCTATTAATTTAATAACAAAGT
GATTATC
Found at i:55687448 original size:12 final size:12
Alignment explanation
Indices: 55687431--55687463 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
55687421 CAGCCTGTCC
55687431 ATATTAATTTTT
1 ATATTAATTTTT
55687443 ATATT-ATTTTT
1 ATATTAATTTTT
55687454 ATA-TAATTTT
1 ATATTAATTTT
55687464 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:55688427 original size:25 final size:25
Alignment explanation
Indices: 55688399--55688483 Score: 89
Period size: 25 Copynumber: 3.1 Consensus size: 25
55688389 AAAATGTTTG
55688399 AAATATTTTAATATAATTTAATATAA
1 AAATATTTTAATATAATTTAATAT-A
*
55688425 AATATTTAATTTTAAAATATAATTTAAAATA
1 AA-A--T-ATTTT--AATATAATTTAATATA
*
55688456 AAATATTTTAATATGATTTAATATA
1 AAATATTTTAATATAATTTAATATA
55688481 AAA
1 AAA
55688484 AGAATTATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
25 17 0.34
26 2 0.04
27 6 0.12
28 1 0.02
29 1 0.02
30 6 0.12
31 3 0.06
32 14 0.28
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (25 bp):
AAATATTTTAATATAATTTAATATA
Found at i:55688459 original size:17 final size:16
Alignment explanation
Indices: 55688408--55688461 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
55688398 GAAATATTTT
55688408 AATATAATTTAATATAA
1 AATATAATTTAA-ATAA
55688425 AATATTTAATTT---TAA
1 AATA--TAATTTAAATAA
55688440 AATATAATTTAAAATAA
1 AATATAATTT-AAATAA
55688457 AATAT
1 AATAT
55688462 TTTAATATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 6 0.19
15 7 0.23
17 12 0.39
19 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATAATTTAAATAA
Found at i:55688494 original size:32 final size:30
Alignment explanation
Indices: 55688401--55688494 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
55688391 AATGTTTGAA
* *
55688401 ATATTTTAATATAATTTAATATAAAATATTT
1 ATATTTTAATAT-ATTTAATATAAAAAAATT
* *
55688432 A-ATTTTAA-A-ATATAATTTAAAATAAA--
1 ATATTTTAATATATTTAATATAAAA-AAATT
55688458 ATATTTTAATATGATTTAATATAAAAAGAATT
1 ATATTTTAATAT-ATTTAATATAAAAA-AATT
55688490 ATATT
1 ATATT
55688495 AAAAATATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
26 1 0.02
27 18 0.37
28 2 0.04
29 2 0.04
30 20 0.41
31 1 0.02
32 5 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (30 bp):
ATATTTTAATATATTTAATATAAAAAAATT
Found at i:55688575 original size:61 final size:61
Alignment explanation
Indices: 55688486--55688620 Score: 193
Period size: 60 Copynumber: 2.2 Consensus size: 61
55688476 ATATAAAAAG
* *
55688486 AATTATATTAAAAATATTATTAAATTATTTATTTTTATTTTTATTAAATTATATTTAATAAT
1 AATTATATTAAAAATATGATTAAATTATTTATTATTA-TTTTATTAAATTATATTTAATAAT
* * *
55688548 AATTATATT-AGAATATGATTAAATTATTTATTATTATTTTATTATATTATTTTTAATAAT
1 AATTATATTAAAAATATGATTAAATTATTTATTATTATTTTATTAAATTATATTTAATAAT
55688608 AATCT-TATTAAAA
1 AAT-TATATTAAAA
55688621 TTTAATAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
60 29 0.45
61 27 0.42
62 9 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (61 bp):
AATTATATTAAAAATATGATTAAATTATTTATTATTATTTTATTAAATTATATTTAATAAT
Found at i:55688591 original size:8 final size:8
Alignment explanation
Indices: 55688499--55688598 Score: 57
Period size: 8 Copynumber: 13.0 Consensus size: 8
55688489 TATATTAAAA
55688499 ATATTATT
1 ATATTATT
*
55688507 AAATTATT
1 ATATTATT
*
55688515 -TATTTTT
1 ATATTATT
*
55688522 ATTTTTATT
1 A-TATTATT
*
55688531 AAATTA-T
1 ATATTATT
*
55688538 AT-TTAAT
1 ATATTATT
*
55688545 A-ATAATT
1 ATATTATT
**
55688552 ATATTAGA
1 ATATTATT
*
55688560 ATATGATT
1 ATATTATT
*
55688568 AAATTATT
1 ATATTATT
55688576 -TATTATT
1 ATATTATT
*
55688583 ATTTTATT
1 ATATTATT
55688591 ATATTATT
1 ATATTATT
55688599 TTTAATAATA
Statistics
Matches: 65, Mismatches: 21, Indels: 12
0.66 0.21 0.12
Matches are distributed among these distances:
6 3 0.05
7 19 0.29
8 37 0.57
9 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
ATATTATT
Found at i:55688798 original size:16 final size:16
Alignment explanation
Indices: 55688777--55688817 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
55688767 ACCAAACAGT
55688777 TCTATTTCATTACAAC
1 TCTATTTCATTACAAC
*
55688793 TCTATTAT-ATTACAGC
1 TCTATT-TCATTACAAC
55688809 TCTATTTCA
1 TCTATTTCA
55688818 ATTAAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.46
Consensus pattern (16 bp):
TCTATTTCATTACAAC
Found at i:55689091 original size:21 final size:22
Alignment explanation
Indices: 55689034--55689091 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
55689024 GTGTAAATAA
55689034 TTTTTTAATATAATTATTATTTT
1 TTTTTTAATATAATTA-TATTTT
55689057 TATTTTTGAA-ATAA-TA-ATTTT
1 T-TTTTT-AATATAATTATATTTT
55689078 TTTTTTACATATAA
1 TTTTTTA-ATATAA
55689092 ACAAATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
19 1 0.03
20 6 0.19
21 10 0.32
23 3 0.10
24 9 0.29
25 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTTAATATAATTATATTTT
Found at i:55691142 original size:40 final size:39
Alignment explanation
Indices: 55691085--55691208 Score: 158
Period size: 40 Copynumber: 3.1 Consensus size: 39
55691075 TGAATGATAC
* *
55691085 CCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTG-TTATAT
* *
55691125 CCGGGCTAAGACCCGAAGGCATTCATGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGTTATAT
* * *
55691165 CCGGGCTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGT-GTTATAT
55691205 CCGG
1 CCGG
55691209 TTGAATCCCG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 70 0.96
41 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGTTATAT
Found at i:55696581 original size:79 final size:81
Alignment explanation
Indices: 55696480--55696664 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
55696470 ACGACTCGCT
** * *
55696480 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
55696543 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
55696560 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
55696624 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
55696640 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55696665 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:55696664 original size:40 final size:39
Alignment explanation
Indices: 55696473--55696664 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
55696463 GGATATAACG
* ** * *
55696473 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
55696513 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
55696553 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
55696592 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
55696632 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
55696665 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:55700980 original size:12 final size:12
Alignment explanation
Indices: 55700963--55700990 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
55700953 TCGAAGGCAT
55700963 TTATGCTAGTGA
1 TTATGCTAGTGA
55700975 TTATGCTAGTGA
1 TTATGCTAGTGA
55700987 TTAT
1 TTAT
55700991 ATCCGGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (12 bp):
TTATGCTAGTGA
Found at i:55701042 original size:40 final size:40
Alignment explanation
Indices: 55700987--55701116 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
55700977 ATGCTAGTGA
*
55700987 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG
1 TTATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTTG
*
55701027 TTATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTA
1 TTATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG
** * * ** *
55701067 CCAAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG
55701107 TTATATCCGG
1 TTATATCCGG
55701117 TTGAATCCCG
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 73 0.96
41 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG
Found at i:55703479 original size:45 final size:45
Alignment explanation
Indices: 55703413--55703534 Score: 149
Period size: 45 Copynumber: 2.7 Consensus size: 45
55703403 TATACACCTA
* ** *
55703413 AAATGAGTATGACCATAGCTGAAAGATGCTATGACATCAGGACA-
1 AAATGAGTAAGACCATAGCTGAAAGACACTATCACATCAGGACAT
*
55703457 AAGATGAGTAAGACCATAGCTGAAAGACACTATCACATCATGACAT
1 AA-ATGAGTAAGACCATAGCTGAAAGACACTATCACATCAGGACAT
* *
55703503 AAATGAGTAAGACAAT-GACTAAAAGACACTAT
1 AAATGAGTAAGACCATAG-CTGAAAGACACTAT
55703535 GGAATCATGG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
44 3 0.04
45 63 0.93
46 2 0.03
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTGAAAGACACTATCACATCAGGACAT
Found at i:55708704 original size:40 final size:39
Alignment explanation
Indices: 55708660--55708841 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
55708650 GTTCAAAACA
* * ** * *
55708660 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
55708700 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
55708740 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
55708779 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
55708818 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
55708842 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:55708771 original size:39 final size:39
Alignment explanation
Indices: 55708690--55708842 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
55708680 TATGGTAACC
* *
55708690 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
55708730 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55708769 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
55708808 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
55708843 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:55716776 original size:40 final size:39
Alignment explanation
Indices: 55716732--55716912 Score: 238
Period size: 39 Copynumber: 4.6 Consensus size: 39
55716722 GTTCAAAACA
* * ** * *
55716732 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
55716772 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
55716812 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
55716851 CCTTCGGGCTTAGCCCGGATATCA-CATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
55716889 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
55716913 CTCGAACATT
Statistics
Matches: 127, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
38 35 0.28
39 52 0.41
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:55716891 original size:38 final size:38
Alignment explanation
Indices: 55716762--55716913 Score: 241
Period size: 39 Copynumber: 3.9 Consensus size: 38
55716752 TATGGTAACC
* *
55716762 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCAC-ACT
*
55716802 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACA-CT
*
55716841 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACACT
55716879 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
55716914 TCGAACATTC
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
38 37 0.35
39 52 0.49
40 17 0.16
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (38 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACACT
Found at i:55716902 original size:77 final size:79
Alignment explanation
Indices: 55716762--55716912 Score: 261
Period size: 77 Copynumber: 1.9 Consensus size: 79
55716752 TATGGTAACC
55716762 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
55716827 CGGATATCATAGCT
66 CGGATATCATAGCT
* * *
55716841 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCAC-ATTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
55716904 CGGATATCA
66 CGGATATCA
55716913 CTCGAACATT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
77 36 0.52
78 16 0.23
79 17 0.25
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (79 bp):
CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
CGGATATCATAGCT
Found at i:55720133 original size:23 final size:23
Alignment explanation
Indices: 55720103--55720151 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
55720093 TACACCACAA
55720103 ATTCTTTACCTGATTCGGGTTGT
1 ATTCTTTACCTGATTCGGGTTGT
55720126 ATTCTTTACCTGATTCGGGTTGT
1 ATTCTTTACCTGATTCGGGTTGT
55720149 ATT
1 ATT
55720152 AACACTAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.49
Consensus pattern (23 bp):
ATTCTTTACCTGATTCGGGTTGT
Found at i:55723935 original size:19 final size:20
Alignment explanation
Indices: 55723911--55723948 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
55723901 GGTACCACCA
55723911 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
55723930 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
55723949 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:55726545 original size:29 final size:29
Alignment explanation
Indices: 55726483--55726585 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
55726473 GTGACGAGAT
* * *
55726483 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
55726512 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
55726541 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
55726570 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
55726586 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:55734022 original size:29 final size:29
Alignment explanation
Indices: 55733960--55734062 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
55733950 GTGACGAGAT
* * *
55733960 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
55733989 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
55734018 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
55734047 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
55734063 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:55736712 original size:13 final size:13
Alignment explanation
Indices: 55736694--55736748 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
55736684 AGATTTTTCT
55736694 TAAATATTATCAC
1 TAAATATTATCAC
*
55736707 TAAATA--ATC-T
1 TAAATATTATCAC
55736717 TAAATATTATCAC
1 TAAATATTATCAC
55736730 TAAATATTATCAC
1 TAAATATTATCAC
55736743 TAAATA
1 TAAATA
55736749 ATTCAAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 6 0.16
11 3 0.08
12 3 0.08
13 25 0.68
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:55736718 original size:23 final size:23
Alignment explanation
Indices: 55736691--55736735 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
55736681 GCTAGATTTT
55736691 TCTTAAATATTATCACTAAATAA
1 TCTTAAATATTATCACTAAATAA
55736714 TCTTAAATATTATCACTAAATA
1 TCTTAAATATTATCACTAAATA
55736736 TTATCACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (23 bp):
TCTTAAATATTATCACTAAATAA
Found at i:55737346 original size:13 final size:13
Alignment explanation
Indices: 55737328--55737362 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
55737318 CTATATACAT
55737328 TTTTTATTTTTTA
1 TTTTTATTTTTTA
*
55737341 TTTTTACTTTTTA
1 TTTTTATTTTTTA
55737354 -TTTTATTTT
1 TTTTTATTTT
55737363 ATTCAAGCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:55751554 original size:25 final size:25
Alignment explanation
Indices: 55751525--55751572 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55751515 TTATAATATG
* * *
55751525 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
55751550 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
55751573 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:55751641 original size:20 final size:20
Alignment explanation
Indices: 55751616--55751674 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
55751606 TAAATATGGT
55751616 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
55751636 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
55751656 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
55751675 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:55751755 original size:23 final size:24
Alignment explanation
Indices: 55751725--55751819 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
55751715 GAGGAAGTGA
55751725 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
55751748 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
55751772 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
55751796 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
55751820 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
23 23 0.36
24 30 0.47
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:55751793 original size:47 final size:49
Alignment explanation
Indices: 55751726--55751819 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
55751716 AGGAAGTGAA
*
55751726 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTG
55751773 AAAGGGCTT-TGGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTAT-GCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
55751820 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 1 0.02
47 19 0.45
48 11 0.26
49 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (49 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:55752062 original size:38 final size:38
Alignment explanation
Indices: 55752011--55752280 Score: 379
Period size: 38 Copynumber: 7.4 Consensus size: 38
55752001 CGTTTACAGT
55752011 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
55752049 AAAGGCTTCGGCCCAG-----T--AATATGAAATATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
55752080 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
55752118 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
55752156 AAAGGCTTCGGCCCAGTAATATGAAATATGAAA-A-G-
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
55752191 --A--CCTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
* *
55752225 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATACGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
55752263 AAAGGGCTACGGCCCAGT
1 AAA-GGCTTCGGCCCAGT
55752281 GCATGATTGA
Statistics
Matches: 208, Mismatches: 9, Indels: 29
0.85 0.04 0.12
Matches are distributed among these distances:
31 55 0.26
32 1 0.00
33 3 0.01
36 3 0.01
37 1 0.00
38 132 0.63
39 13 0.06
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (38 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
Found at i:55752087 original size:69 final size:71
Alignment explanation
Indices: 55752011--55752280 Score: 324
Period size: 69 Copynumber: 3.8 Consensus size: 71
55752001 CGTTTACAGT
55752011 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAG-T-AATATGAA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTTAAATATGAA
*
55752074 ATATGA
66 ACATGA
55752080 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAG---T-T-AAAT
55752145 ATGAAACATGA
61 ATGAAACATGA
* *
55752156 AAAGGCTTCGGCCCAGTAATATGAAATATGAAA-A-G---A--CCTCGGCCCAGTATTATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAG---T-T-AAAT
55752214 ATGAAACATGA
61 ATGAAACATGA
* * *
55752225 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATACGAAAAGGGCTACGGCCCAGT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAA-GGCTTCGGCCCAGT
55752281 GCATGATTGA
Statistics
Matches: 180, Mismatches: 6, Indels: 25
0.85 0.03 0.12
Matches are distributed among these distances:
69 118 0.66
70 1 0.01
71 2 0.01
74 4 0.02
75 1 0.01
76 45 0.25
77 9 0.05
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (71 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTTAAATATGAA
ACATGA
Found at i:55752146 original size:107 final size:107
Alignment explanation
Indices: 55752011--55752280 Score: 486
Period size: 107 Copynumber: 2.5 Consensus size: 107
55752001 CGTTTACAGT
55752011 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
* *
55752076 ATGAAAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
66 ATGAAAAGACCTCGGCCCAGTATTATGAAATATGAAACATGA
55752118 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
55752183 ATGAAAAGACCTCGGCCCAGTATTATGAAATATGAAACATGA
66 ATGAAAAGACCTCGGCCCAGTATTATGAAATATGAAACATGA
* * *
55752225 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATACGAAAAGGGCTACGGCCCAGT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAA-GGCTTCGGCCCAGT
55752281 GCATGATTGA
Statistics
Matches: 157, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 144 0.92
108 13 0.08
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (107 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
ATGAAAAGACCTCGGCCCAGTATTATGAAATATGAAACATGA
Found at i:55753439 original size:17 final size:19
Alignment explanation
Indices: 55753397--55753440 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
55753387 ACGAAATTTT
*
55753397 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
55753416 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
55753434 AA-TATTA
1 AATTATTA
55753441 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:55753550 original size:15 final size:15
Alignment explanation
Indices: 55753532--55753560 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55753522 ATATTTTTAA
55753532 AATTATTATTATTAT
1 AATTATTATTATTAT
55753547 AATTATTATTATTA
1 AATTATTATTATTA
55753561 GATAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTATTATTAT
Found at i:55757622 original size:39 final size:39
Alignment explanation
Indices: 55757541--55757703 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
55757531 TATGGTAACC
** *
55757541 CGCACAAACGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
55757581 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55757620 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55757659 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
55757698 CGCACA
1 CGCACA
55757704 TTCATTCACA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 99 0.86
40 16 0.14
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:55764649 original size:40 final size:39
Alignment explanation
Indices: 55764605--55764797 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
55764595 GTTCAAAACA
* * ** * *
55764605 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
55764645 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
55764685 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
55764724 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
55764763 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
55764798 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:55764716 original size:39 final size:39
Alignment explanation
Indices: 55764635--55764797 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
55764625 TATGGTAACC
* *
55764635 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
55764675 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55764714 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55764753 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
55764792 CGCACA
1 CGCACA
55764798 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:55765822 original size:60 final size:59
Alignment explanation
Indices: 55765746--55765880 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 59
55765736 AACTGTGTTA
* * * *
55765746 ATATGGGCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATAAACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAACACTG
* * *
55765806 ATATGGGCTAGGCCCAATAAACTCTGATACTGTAAGGGGCTATGGCCCAGATTAACATTG
1 ATATGGGCTAGGCCCAATAAACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAACACTG
55765866 ATATGGGCTAAGGCC
1 ATATGGGCT-AGGCC
55765881 TAGTTAACAC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 1 0.02
60 50 0.78
61 13 0.20
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATAAACTCTGATATGTAAAGGGCTACGGCCCAGATTAACACTG
Done.